Whenever one of these two options is enabled:
focus-follows-mouse
mouse-autoselect-window
a floating window causes the cursor to warp to some weird coordinates. I think this commit 9742498 is the culprit, because it used to work fine before.
Namely, this behaviour is triggered by select-frame-set-input-focus, perhaps because the call happens before xcb's position requests are flushed, which makes Emacs warp the cursor to somewhere on the edge of the screen.
This fixes the issue:
(defun my/exwm-floating--set-floating-around (orig-fun &rest args)
(let ((focus-follows-mouse nil)
(mouse-autoselect-window nil))
(apply orig-fun args)))
(with-eval-after-load 'exwm
(advice-add 'exwm-floating--set-floating :around
#'my/exwm-floating--set-floating-around))
I would have submitted a patch but I don't have the copyright papers.